[adegenet-forum] Fw: df2genind function unexpected behavior

[Tagliamonte,Massimiliano S]

Thanks for the feedback to the both of you,

Nice to know it's not just me ;) 

Cheers,
Max

________________________________________
From: adegenet-forum-bounces at r-forge.wu-wien.ac.at <adegenet-forum-bounces at r-forge.wu-wien.ac.at> on behalf of Roman Luštrik <roman.lustrik at biolitika.si>
Sent: Wednesday, January 4, 2017 11:02 AM
To: Vojtěch Zeisek
Cc: adegenet-forum at r-forge.wu-wien.ac.at
Subject: Re: [adegenet-forum] df2genind function unexpected behavior

In my experience, this is very common. Which is important to have a self contained example. I do this for my analyses all the time.

Cheers,
Roman

----
In god we trust, all others bring data.

----- Original Message -----
From: "Vojtěch Zeisek" <vojta at trapa.cz>
To: adegenet-forum at lists.r-forge.r-project.org
Sent: Wednesday, January 4, 2017 4:17:19 PM
Subject: Re: [adegenet-forum] df2genind function unexpected behavior

Hello,
if You load new library and it by coincidence contain a function with same
name as one of the already loaded functions, the old one is replaced by the
new one. When loading such library, the R says which functions are replaced.
This can be common source of problems. Check it.
Sincerely,
V.

Dne středa 4. ledna 2017 15:05:03 CET, Tagliamonte,Massimiliano S napsal(a):
> Thank you for your help, Roman,
>
> By asking me to provide an example you made me realize something. I tried
> again this morning, with exactly the same commands, and could not reproduce
>  the issue. This is weird. It is not the first time it happens though, i.e.
> getting unexpected behavior in R which I could not replicate after
> rebooting. I have no idea what the cause could be. Some of the packages I
> had loaded yesterday (apart from Adegenet) were not loaded today. I guess
> I'll have to be even more paranoid and check that each step of my analysis
> does what is supposed to be doing.
>
> Cheers,
>
> Max
>
> ________________________________
> From: Roman Luštrik <roman.lustrik at biolitika.si>
> Sent: Tuesday, January 3, 2017 5:44 PM
> To: Tagliamonte,Massimiliano S
> Cc: adegenet-forum at lists.r-forge.r-project.org
> Subject: Re: [adegenet-forum] df2genind function unexpected behavior
>
> Can you provide a reproducible example?
>
> FWIW, you can use accessor functions like `tab(genind_obj)` or access the
> other slot through `other(genind_obj)`, e.g.
>
> library(adegenet)
>
> data(nancycats)
>
> other(nancycats)$xy
>
> or assigning things
>
> other(nancycats)$xy <- xy_object
>
> To access genotypes, you can use
>
> tab(nancycats)
>
> Cheers,
> Roman
>
> ________________________________
> From: "Tagliamonte,Massimiliano S" <mstagliamonte at ufl.edu>
> To: "adegenet-forum at lists.r-forge.r-project.org"
> <adegenet-forum at r-forge.wu-wien.ac.at> Sent: Tuesday, January 3, 2017
> 10:36:20 PM
> Subject: Re: [adegenet-forum] df2genind function unexpected behavior
>
> Update:
>
> OK, I have replaced the dots (".") in the names with "_", now the order of
> the isolates is maintained. I'll have to keep in mind this behavior. I
> guess it's a bad idea to introduce special characters in my data in R.
--
Vojtěch Zeisek
https://trapa.cz/en/

Department of Botany
Faculty of Science, Charles University
Benátská 433/2, Prague, 12801, CZ
https://www.natur.cuni.cz/biology/botany/

Institute of Botany, Academy of Sciences
Zámek 1, Průhonice, 25243, CZ
http://www.ibot.cas.cz/en/

Czech Republic

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